[English] 日本語
Yorodumi
- PDB-3hj2: Crystal structure of covalent dimer of HNP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hj2
TitleCrystal structure of covalent dimer of HNP1
ComponentsHUMAN NEUTROPHIL PEPTIDE 1
KeywordsANTIMICROBIAL PROTEIN / defensin / antimicrobial / chemotactic / cationic / Cys-rich / covalent dimer / synthetic / Antibiotic / Antiviral defense / Disulfide bond / Fungicide / Phosphoprotein / Secreted
Function / homology
Function and homology information


pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa ...pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / collagen-containing extracellular matrix / defense response to virus / killing of cells of another organism / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Defensin propeptide / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Neutrophil defensin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLubkowski, J. / Pazgier, M. / Lu, W.
CitationJournal: To be Published
Title: What Dictates the Multifaced Functions of the Human alpha-Defensin HNP1?
Authors: Wei, G. / de Leeuw, E. / Pazgier, M. / Rajabi, M. / Li, J. / Zou, G. / Ericksen, B. / Wu, Z. / Yuan, W. / Szmacinski, H. / Lu, W.-Y. / Lubkowski, J. / Lehrer, R.L. / Lu, W.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HUMAN NEUTROPHIL PEPTIDE 1
B: HUMAN NEUTROPHIL PEPTIDE 1


Theoretical massNumber of molelcules
Total (without water)7,3392
Polymers7,3392
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-12 kcal/mol
Surface area4590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.07, 49.37, 24.99
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein/peptide HUMAN NEUTROPHIL PEPTIDE 1 / Neutrophil defensin 1 / HNP-1 / HP-1 / HP1 / Defensin / alpha 1 / HP 1-56 / Neutrophil defensin 2 / ...Neutrophil defensin 1 / HNP-1 / HP-1 / HP1 / Defensin / alpha 1 / HP 1-56 / Neutrophil defensin 2 / HNP-2 / HP-2 / HP2


Mass: 3669.358 Da / Num. of mol.: 2 / Fragment: Residues 65-94 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P59665
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAN ARTIFICIAL N-TERMINAL CGG EXTENSION DESIGNED TO COVALENTLY LINK (CYS-CYS) MONOMERS OF HNP1

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Na-citrate (pH 5.6), 0.2 M NH4-acetate, 30% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2007
Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220)
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→24.68 Å / Num. all: 11611 / Num. obs: 11611 / % possible obs: 96.3 % / Observed criterion σ(F): -1.7 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 22.5
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 17.8 / Num. unique all: 1171 / Rsym value: 0.114 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0057refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dfn

1dfn


Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / SU B: 2.655 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23578 579 5 %RANDOM
Rwork0.19886 ---
all0.20059 10987 --
obs0.20059 10987 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.827 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.72 Å2
Refine analyzeLuzzati coordinate error obs: 0.248 Å / Luzzati d res low obs: 15 Å
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms487 0 0 51 538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022505
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.935685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.617564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.59417.89519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3981568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.451157
X-RAY DIFFRACTIONr_chiral_restr0.1360.266
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021393
X-RAY DIFFRACTIONr_mcbond_it2.1081.5322
X-RAY DIFFRACTIONr_mcangle_it2.8932499
X-RAY DIFFRACTIONr_scbond_it3.5123183
X-RAY DIFFRACTIONr_scangle_it4.5584.5186
X-RAY DIFFRACTIONr_rigid_bond_restr1.9943505
X-RAY DIFFRACTIONr_sphericity_free10.232351
X-RAY DIFFRACTIONr_sphericity_bonded5.1543487
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 31 -
Rwork0.192 819 -
obs-850 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4972-0.56390.964410.0792-0.85162.43360.0043-0.04830.00710.4582-0.0008-0.2318-0.05030.1399-0.0036-0.10930.01020.0135-0.11660.0107-0.1436-18.7710.4964.063
211.5009-3.17941.36783.9254-3.18163.4533-0.27620.17440.61650.18540.0123-0.357-0.19720.01610.2638-0.1130.0166-0.0498-0.1045-0.0284-0.1035-12.5554.905-4.732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 8
2X-RAY DIFFRACTION1A9 - 15
3X-RAY DIFFRACTION1A16
4X-RAY DIFFRACTION1A17 - 33
5X-RAY DIFFRACTION2B3 - 8
6X-RAY DIFFRACTION2B9 - 15
7X-RAY DIFFRACTION2B16
8X-RAY DIFFRACTION2B17 - 33

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more